Abstract

In this thesis molecular dynamics simulations, in conjunction with the complementary methods of docking and QM-MM, are used, and further developed, to study two unusual polypeptide systems: the conformational preferences of isomers of an antibiotic peptide and the binding behaviour of a human transporter protein. The antibiotic peptides are analogues of a naturally occurring antibacterial called nisin which has a biological function dependent on the formation of five macrocyclic rings closed by a thioether bond between modified L-amino and D-amino residues. We propose analogues where the thioether bond is replaced by a disulfide bond between cysteine residues and the chirality of the cysteines is altered. The conformational preferences of the nisin analogues, and the dependence of ring formation on cysteine chirality, are characterised using molecular dynamics. An analogue (D-Cys3-D-Cys7-L-Cys8-L-Cys11) is identified that favours the simultaneous formation of the S3-S7 and S8-S11 disulfide bonds and has an RMSD of 0.6 Å to 1.7 Å between the centroids from clustering the MD trajectories and an NMR structure of wt-nisin. The nisin analogues contain unusual D-amino residues and using explicit solvent MD simulations of four polypeptides, it is shown that the (φ, ψ) → (-φ, -ψ) transformation of the CMAP term in the CHARMM potential energy function leads to sampling of conformations which are closest to X-ray crystallographic structures for D-amino residues and that the standard CMAP correction destabilises D-amino β-sheets and β-turns.

The ileal lipid binding protein (ILBP) shows cooperative binding comparable to haemoglobin and unusual site selectivity where one ligand will completely displace another from a binding site, despite both sites having an affinity for each ligand type and the ligands only differing by a single hydroxyl group. A probable location of the third binding site of ILBP is identified which has a role in the allosteric binding mechanism. MD simulations indicate that binding to this exterior site induces changes in the orientation of the α-helices with respect to the β-barrel by ~10°. An energetic mechanism of site selectivity for ILBP is proposed using evidence from MD simulations. The higher hydrophobicity of chenodeoxycholic acid leads it to sit deeper in the binding cavity and interact with Gln-51. This causes the cholic acid ligand to be deeper and induces the helices to move closer to the β-barrel, preventing further ligand exchange.